Investigating Phase Separations as a Mechanism of Genome Compartmentalization Through In-vivo Experiments

New York University, New York NY

Investigators

Abstract

The human genome consists of two meters of DNA stored inside the cell nucleus barely 10 micrometers in diameter. The DNA molecule is packed in a structure known as chromatin, whose organization inside the cell nucleus directly affects the genome’s function, which in turn is critical for the proper function of the cell. Hence, elucidating the principles underlying chromatin organization is fundamental to understanding the genome in health and disease, as well as designing new active and smart materials. Yet, the physical principles behind the genome’s organization remain elusive. The goal of this project is to generate a mechanistic picture of chromatin organization inside live human cells by combining quantitative experimental approaches and theory from relevant areas of physics. As a part of this project, the PI will develop educational and outreach components with focus on recruitment and retention in physics across different education and career stages. This project will also provide novel educational and training opportunities for undergraduate and graduate students, who will receive training in advanced optical microscopy techniques, small angle X-ray scattering, image processing, and data analysis as well as polymer physics, biophysics, and statistical mechanics. The structure, organization and dynamics of chromatin inside the cell nucleus control all aspects of DNA biology. Chromatin fiber is hierarchically folded with increasing length scale into loops, topologically associated domains, A and B compartments (transcriptionally active and inactive genomic parts) and finally chromosome territories. Moreover, chromatin is heterogeneously distributed across the nucleus into two types of compartments: euchromatin, less dense and predominantly transcriptionally active regions, and heterochromatin, denser regions containing mainly silenced genes. Despite this detailed picture of the genome organization, its underlying physical principles remain unknown. Moreover, the genome is immersed in a solvent, the nucleoplasm, which was shown to organize itself, by undergoing liquid-liquid phase separations, and forming functional liquid condensates. How to reconcile the genomic and nucleoplasmic spatial organization remains an open question. The overall goal of this project is to reveal the physical principles behind the genome’s organization using state-of-the-art in-vivo experimental approaches and data analytics, which will directly inform development of new models and theories. By combining the latest quantitative techniques from polymer physics, soft condensed matter physics, biophysics and cell biology, this project will investigate the mechanism/s behind the genome compartmentalization and elucidate the physical laws underlying such organization. These measurements will provide fundamental insights into phase separation as the guiding physical principle for compartmentalization of the genome. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.